12.28.11 9:45 AM ET

When Defense Secretary Leon Panetta opined earlier this month that an Israeli attack on Iran’s nuclear facilities could “consume the Middle East in a confrontation and a conflict that we would regret,” the Israelis went ballistic behind the scenes. Michael Oren, Israel’s ambassador to Washington, lodged a formal diplomatic protest known as a demarche. And the White House was thrust into action, reassuring the Israelis that the administration had its own “red lines” that would trigger military action against Iran, and that there is no need for Jerusalem to act unilaterally.

Panetta’s seemingly innocent remarks on Dec. 2 triggered the latest drama in the tinder-box relationship that the Obama administration is trying to navigate with Prime Minister Benjamin Netanyahu’s government. With Republicans lining up to court Jewish donors and voters in America in 2012, Obama faces a tricky election-year task of ensuring Iran doesn’t acquire a nuclear bomb on his watch while keeping the Israelis from launching a preemptive strike that could inflame an already teetering Middle East.

The stakes are immensely high, and the distrust that Israelis feel toward the president remains a complicating factor. Those sentiments were laid bare in a speech Netanyahu’s minister of strategic affairs, Moshe Ya’alon, gave on Christmas Eve in Jerusalem, in which he used Panetta’s remarks to cast doubt on the U.S.’s willingness to launch its own military strike.

Ya’alon told the Anglo-Likud, an organization within Netanyahu’s Likud party that caters to native English speakers, that the Western strategy to stop Iran’s drive for nuclear weapons must include four elements, with the last resort being a military strike.

“The fourth element of this combined strategy is the credible military strike,” Ya’alon said, according to a recording of the speech provided to The Daily Beast. “There is no credible military action when we hear leaders from the West, saying, ‘this is not a real option,’ saying, ‘the price of military action is too high.’”

The lack of trust between the Israeli and American leaders on Iran has been a sub-rosa tension in the relationship since 2009. Three U.S. military officials confirm to The Daily Beast that analysts attached to the Office of the Secretary of Defense are often revising estimates trying to predict what events in Iran would trigger Prime Minister Netanyahu to authorize a military attack on the country’s nuclear infrastructure. Despite repeated requests going back to 2009, Netanyahu’s government has not agreed to ask the United States for permission or give significant advanced warning of any pending strike.

The sensitive work of trying to get both allies on the same page intensified this month. Israeli Defense Minister Ehud Barak visited Washington last week to go over Iran issues; and the undersecretary of state for political affairs, Wendy Sherman, and a special arms control adviser to Secretary of State Hillary Clinton, Robert Einhorn, were in Israel last week to discuss Iran as well. Panetta for his own part has revised his tone on the question of Iran’s nuclear program, telling CBS News last week that the United States was prepared to use force against Iran to stop the country from building a nuclear weapon.

The new diplomacy has prompted new conversations between the United States and Israel over what the triggers—called “red lines” in diplomatic parlance—would be to justify a pre-emptive attack on Iran’s nuclear facilities.

Matthew Kroenig, who served as special adviser on Iran to the Office of the Secretary of Defense between July 2010 and July 2011, offered some of the possible “red lines” for a military strike in a recent Foreign Affairs article he wrote. He argued that the U.S should attack Iran’s facilities if Iran expels international nuclear weapons inspectors, begins enriching its stockpiles of uranium to weapons-grade levels of 90 percent, or installs advanced centrifuges at its main uranium-enrichment facility in Qom.

In an interview with The Daily Beast, Kroenig also noted that Iran announced in 2009 that it was set to construct 10 new uranium enrichment sites. “I doubt they are building ten new sites, but I would be surprised if Iran was not racing to build some secret enrichment facilities,” Kroenig said. “Progress on new facilities would be a major factor in our assessment of Iran’s nuclear program and shape all aspects of our policy towards this including the decision to use force.”

Until recently, current and former Obama administration officials would barely broach the topic in public, only hinting vaguely that all options are on the table to stop Iran’s program. Part of the reason for this was that Obama came into office committed to pursuing negotiations with Iran. When the diplomatic approach petered out, the White House began building international and economic pressure on Iran, often in close coordination with Israel.

All the while, secret sabotage initiatives like a computer worm known as Stuxnet that infected the Siemens-made logic boards at the Natanz centrifuge facility in Iran, continued apace. New U.S. estimates say that Stuxnet delayed Iran’s nuclear enrichment work by at most a year, despite earlier estimates that suggested the damage was more extensive.

Last week in a CBS interview, Panetta said Iran’s development of a nuclear weapon is a “red line.” White House advisers have more recently broached the subject more specifically in private conversations with outside experts on the subject.

Patrick Clawson, the director of research for the Washington Institute for Near East Policy said, “If Iran were found to be sneaking out or breaking out then the president’s advisers are firmly persuaded he would authorize the use of military force to stop it.” But Clawson added, “The response they frequently get from the foreign policy experts is considerable skepticism that this is correct, not that these people are lying to us, but rather when the occasion comes we just don’t know how the president will react.”

Henry Sokolski, the executive director the Nonproliferation Policy Education Center, said “You don’t propose and go about doing an oil embargo unless you are serious about taking the next step, and the next step for the administration is clearly some form of military action, and people who have left the administration like Dennis Ross have made it clear that this is precisely what’s on this administration’s mind.”

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Ross did not respond to emails and phone calls requesting comment.

Ironically, Panetta often is the official the Obama administration uses to engage Israel. “Panetta has been straightforward with the Israelis and they seem to appreciate that,” one senior administration official said. “The Israelis view Panetta as an honest broker.” In some ways that is why his remarks stung Netanyahu’s government so much.

Complicating matters, the Dec. 2 remarks also came at the same time a high-level delegation of Israeli diplomats, military officers and intelligence officials were in Washington for an annual meeting called the strategic dialogue. At the meeting, the Israeli side offered a new presentation on Iran’s nuclear program suggesting that Iran’s efforts to build secret reactors for producing nuclear fuel were further along than the United States has publicly said. Some of the intelligence was based on soil samples collected near the suspected sites.

Part of the issue now between the United States and Israel are disagreements over such intelligence. The Israelis and the U.S. both believe that Iran suspended its work on weaponization, or the research and testing on how to fit an atomic explosion inside a warhead, in 2003 shortly after the U.S. invasion of Iraq.

The Israelis, however, say the Iranians started that work again in 2005, according to Israeli officials and Ya’alon, who said this in his speech on Christmas Eve. The 2007 and 2011 U.S. national intelligence estimates for Iran say this weaponization work remains suspended.

The Israelis also say a recent document uncovered by the International Atomic Energy Agency (IAEA) that shows detailed plans for constructing a “neutron initiator,” or a pellet that sits at the middle of the nuclear core and is crushed by high explosives in a nuclear explosion, is evidence that Iran is continuing its weaponization work. The latest IAEA report released in November said members states had shared intelligence alleging that Iran had conducted explosive tests associated with nuclear weapons research.

A senior administration official told The Daily Beast, “Both Americans and Israelis agree that some research and design work is probably continuing in the event the Iranians decide to move ahead with weaponization.”

The intelligence disagreement is significant in part because one of the factors in drawing up red lines on Iran’s program is how much progress Iran has made in constructing secret enrichment facilities outside of Natanz, where IAEA inspectors still monitor the centrifuge cascades. In 2009, the Obama administration exposed such a facility carved into a mountain outside of the Shiite holy city of Qom. The IAEA has chastised the Iranians for not fully disclosing their work on the Qom site until the United States forced the regime’s hand.